pepStat citations

[…] pathicity. Additionally, the properties of sequences including aromatic and aliphatic, basic and acidic sequences with average number of polar and nonpolar amino acids were determined by using EMBOOS PepStat []. To discover the position of these proteins with predicted signature sequences, TMHMM [], HMMTOP [] and SOSUI-GramN [] were used, while subcellular localization of proteins was determined b […]

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Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids

2016

Sci Rep

PMCID: 5138847

PMID: 27922051

DOI: 10.1038/srep38302

[…] he atomic coordinates of DrUox. The number of cysteines in Uox proteins of different taxonomic divisions was determined for 1385 sequences clustered at 80% similarity with the cdhit program using the pepstat program of the Emboss package. Data were plotted using the geom_boxplot and geom_jitter functions of the ggplot2 library of the R package. […]

[…] noic acid dehalogenase from bacterial and fungal sources were retrieved from the NCBI database (http://www.ncbi.nlm.nih.gov/protein/). The amino acid composition of these sequences was computed using PEPSTAT module integrated in the EMBOSS software []. Multiple sequence alignment for individual profiles was performed using MUSCLE and phylogenetic analysis using MEGA 6 software []. The discovered m […]

[…] mologous two hundred mesophilic proteins (Table A in ) were downloaded and the percentage of 20 amino acids in each protein was calculated by accessing the website http://www.ebi.ac.uk/Tools/services/Pepstat []. The frequency zone was arranged in ascending order. Here, the Sturges formula (k = 1+3.322 log10 N) was used to find the class interval and desirable number of groups into which the distri […]

[…] his is
required to find out the surface membrane proteins which
could be probable drug targets. Further these surface
membrane pathway protein sequences were characterized by
using Peptide Statistic (PEPSTAT) program which is available
online via European Molecular Biology Open Software Suite
(EMBOSS) web server []. […]

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A top down approach to classify enzyme functional classes and sub classes using random forest

2012

EURASIP J Bioinform Syst Biol

PMCID: 3351021

PMID: 22376768

DOI: 10.1186/1687-4153-2012-1

[…] ical information about an enzyme and if coupled with structural characteristics, can contribute to a more robust and accurately predicting model. By using 73 different features extracted using EMBOSS PEPSTAT and ProtParams tool, we have tried to highlight how existing tools can be re-used and extended to address interesting problems in Bioinformatics. The results from the experiments demonstrate t […]